6UPW: Metavinculin ABD-F-actin complex

Metavinculin ABD-F-actin complex. Determined by electron microscopy at 2.9 Å resolution. Released 30 Sept 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Gallus gallus
Chains: 7
Atoms: 16,896
Mol. weight: 459.55 kDa
Ligands: MG, ADP
Released: 30 Sept 2020

Explore 6UPW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UPW contains 139 α-helices and 98 β-strands across 7 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	13
β-strand	16-21	6	13
β-strand	29-32	4	13
β-strand	35-38	4	14
β-strand	41	1	5
β-strand	53	1	14
α-helix	57-60	4
α-helix	62-64	3
β-strand	65-68	4	14
β-strand	71-72	2	15
β-strand	75-76	2	15
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	13
α-helix	113-125	13
β-strand	131-136	6	13
α-helix	137-143	7
β-strand	150-155	6	16
β-strand	160-166	7	16
β-strand	169-170	2	16
α-helix	172-174	3
β-strand	176-178	3	16
α-helix	182-191	10
α-helix	206-216	11
α-helix	223-232	10
β-strand	238-241	4	17
β-strand	247-250	4	17
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	271-273	3
α-helix	274-282	9
α-helix	290-294	5
β-strand	297-300	4	16
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	16
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-354	3
β-strand	357-358	2	13
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain B: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	7
β-strand	16-21	6	7
β-strand	29-32	4	7
β-strand	35-38	4	8
β-strand	41	1	9
β-strand	53	1	8
α-helix	57-60	4
α-helix	62-64	3
β-strand	65-68	4	8
β-strand	71-72	2	10
β-strand	75-76	2	10
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	7
α-helix	114-125	12
β-strand	131-136	6	7
α-helix	137-143	7
β-strand	150-155	6	11
β-strand	160-166	7	11
β-strand	169-170	2	11
α-helix	172-174	3
β-strand	176-178	3	11
α-helix	182-192	11
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	12
β-strand	247-250	4	12
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-282	9
α-helix	290-294	5
β-strand	297-300	4	11
α-helix	309-318	10
α-helix	326-327	2
β-strand	329-330	2	11
α-helix	335-337	3
α-helix	338-347	10
α-helix	351-354	4
β-strand	357-358	2	7
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain C: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
β-strand	41	1	3
β-strand	53	1	2
α-helix	57-60	4
α-helix	62-64	3
β-strand	65-68	4	2
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-143	7
β-strand	150-155	6	5
β-strand	160-166	7	5
β-strand	169-170	2	5
α-helix	172-174	3
β-strand	176-178	3	5
α-helix	182-192	11
α-helix	206-216	11
α-helix	223-232	10
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-282	9
α-helix	287-289	3
α-helix	291-294	4
β-strand	297-300	4	5
α-helix	309-318	10
β-strand	329-330	2	5
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-354	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain D: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	18
β-strand	16-21	6	18
β-strand	29-32	4	18
β-strand	35-38	4	19
β-strand	53	1	19
α-helix	57-60	4
α-helix	62-64	3
β-strand	65-68	4	19
β-strand	71-72	2	20
β-strand	75-76	2	20
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	18
α-helix	113-125	13
β-strand	131-136	6	18
α-helix	137-143	7
β-strand	149-155	7	9
β-strand	160-166	7	9
β-strand	169-170	2	9
β-strand	176-178	3	9
α-helix	182-192	11
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	21
β-strand	247-250	4	21
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-283	10
α-helix	291-294	4
β-strand	297-300	4	9
α-helix	302-304	3
α-helix	309-318	10
α-helix	326-327	2
β-strand	329-330	2	9
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-354	3
β-strand	357-358	2	18
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain E: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	22
β-strand	16-21	6	22
β-strand	29-32	4	22
β-strand	35-38	4	23
β-strand	53	1	23
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	23
β-strand	71-72	2	24
β-strand	75-76	2	24
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	22
α-helix	113-125	13
β-strand	131-136	6	22
α-helix	137-143	7
β-strand	150-155	6	3
β-strand	160-166	7	3
β-strand	169-170	2	3
α-helix	172-174	3
β-strand	176-178	3	3
α-helix	182-192	11
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	25
β-strand	247-250	4	25
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-282	9
α-helix	291-294	4
β-strand	297-300	4	3
α-helix	302-304	3
α-helix	309-318	10
β-strand	329-330	2	3
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-354	3
β-strand	357-358	2	22
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain L: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	986-1004	19
α-helix	1009-1011	3
α-helix	1013-1019	7
α-helix	1022-1039	18
α-helix	1043-1052	10
α-helix	1056-1073	18
α-helix	1083-1119	37
α-helix	1123-1125	3

Chain M: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	986-1004	19
α-helix	1013-1019	7
α-helix	1022-1037	16
α-helix	1043-1053	11
α-helix	1056-1059	4
α-helix	1061-1064	4
α-helix	1066-1073	8
α-helix	1083-1119	37
α-helix	1128-1130	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	L, M	protein	1134	Homo sapiens	P18206 (AlphaFold model)
Actin, alpha skeletal muscle	A, B, C, D, E	protein	375	Gallus gallus	P68139 (AlphaFold model)

Sequence of entity 1 (L, M), FASTA

>6UPW_1 Vinculin (chains L, M)
MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKE
TVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTS
DLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQ
ELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAE
INEIIRVLQLTSWDEDAWASKDTEAMKRALASIDSKLNQAKGWLRDPSASPGDAGEQAIR
QILDEAGKVGELCAGKERREILGTCKMLGQMTDQVADLRARGQGSSPVAMQKAQQVSQGL
DVLTAKVENAARKLEAMTNSKQSIAKKIDAAQNWLADPNGGPEGEEQIRGALAEARKIAE
LCDDPKERDDILRSLGEISALTSKLADLRRQGKGDSPEARALAKQVATALQNLQTKTNRA
VANSRPAKAAVHLEGKIEQAQRWIDNPTVDDRGVGQAAIRGLVAEGHRLANVMMGPYRQD
LLAKCDRVDQLTAQLADLAARGEGESPQARALASQLQDSLKDLKARMQEAMTQEVSDVFS
DTTTPIKLLAVAATAPPDAPNREEVFDERAANFENHSGKLGATAEKAAAVGTANKSTVEG
IQASVKTARELTPQVVSAARILLRNPGNQAAYEHFETMKNQWIDNVEKMTGLVDEAIDTK
SLLDASEEAIKKDLDKCKVAMANIQPQMLVAGATSIARRANRILLVAKREVENSEDPKFR
EAVKAASDELSKTISPMVMDAKAVAGNISDPGLQKSFLDSGYRILGAVAKVREAFQPQEP
DFPPPPPDLEQLRLTDELAPPKPPLPEGEVPPPRPPPPEEKDEEFPEQKAGEVINQPMMM
AARQLHDEARKWSSKPGIPAAEVGIGVVAEADAADAAGFPVPPDMEDDYEPELLLMPSNQ
PVNQPILAAAQSLHREATKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGTKRALIQCAK
DIAKASDEVTRLAKEVAKQCTDKRIRTNLLQVCERIPTISTQLKILSTVKATMLGRTNIS
DEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKTPWYQ

Sequence of entity 2 (A, B, C, D, E), FASTA

>6UPW_2 Actin, alpha skeletal muscle (chains A, B, C, D, E)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5

Primary citation

Molecular mechanism for direct actin force-sensing by alpha-catenin. Mei, L., Espinosa de Los Reyes, S., Reynolds, M.J. et al. Elife (2020) 9. DOI 10.7554/eLife.62514 · PubMed

Other PDB entries of the same protein (UniProt P18206 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LN2 1.0 Å, The second SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin
4LNP 1.41 Å, The first SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin
3RF3 1.61 Å, Shigella IpaA-VBS3 in complex with human vinculin
1YDI 1.8 Å, Human Vinculin Head Domain (VH1, 1-258) in Complex with Human Alpha-Actinin's…
3S90 1.97 Å, Human vinculin head domain Vh1 (residues 1-252) in complex with murine talin (VBS33;…
3TJ5 1.99 Å, human vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding…
3MYI 2.2 Å, Human metavinculin tail domain
4DJ9 2.25 Å, Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin…
1RKE 2.35 Å, Human vinculin head (1-258) in complex with human vinculin tail (879-1066)
1SYQ 2.42 Å, Human vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin…
5L0I 2.45 Å, Human metavinculin MVt R975W cardiomyopathy-associated mutant (residues 959-1134)
3VF0 2.54 Å, Raver1 in complex with metavinculin L954 deletion mutant

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